The president has faced strong opposition from legislators, including from his own Democratic party, to the transfer of prisoners to US soil for detention and trial.
In May, congress demanded a detailed plan on closing the prison before it would grant Obama the necessary funds to do so.
'Soon as possible'
A separate government task force reviewing rules of the interrogration of detainees also fell short of its Tuesday deadline and has been granted an extra two months to submit a final report, senior administration officials said.
But that panel did issue a five-page interim report late on Monday that said "where appropriate, prosecution of those responsible must occur as soon as possible, whether in federal court or before a military commission".
"Justice cannot be done, however, unless those who are accused of crimes are proved guilty beyond a reasonable doubt in a court of law that affords them a full and fair opportunity to contest the charges against them," it said.
Obama has ordered that the Guantanamo be closed by January 2010 but, six months on, fewer than 20 detainees have been transferred and 229 remain in the prison.
A senior administration official has said the justice department is considering prosecuting about 30 others in federal courts, and another 30 or so could face trial by military commissions.
David Remes, a US lawyer representing 18 men still being held in Guantanamo Bay, told Al Jazeera that the Obama administration had few options when it comes to dealing with Guantanamo detainees.
"President Obama is boxed in ... there is simply no place to send the men," he said.
"The process President Obama set in place to review the status of each man was very elegant in theory, but it took so long that Republicans were able to mobilise a very effective opposition," he said.
Government lawyers have so far finished the reviews of more than half of the detainees. More than 50 suspects have been cleared for transfer to other countries.
"This has become a political morass for the president," Remes said.
"I don't think this is going to be forgotten, I just think the struggle is going to continue a lot longer than we thought it would."
Sahr Muhammed Ally, a lawyer who works on US counter-terrorism and national security policies, told Al Jazeera that Guantanamo is a "great legal mess" that the Bush administration left for the Obama administration.
"We have made several recommendations to the [Obama] administration that individuals being held in Guantanamo be prosecuted in civilian federal courts in the US, but we have heard they are doing a case by case analysis on each prisoner to see whether [this can happen]," she said.
"It doesn't help that congress is blocking funding to transfer any individuals from Guantanamo to the US mainland."
Some of the detainees will be held indefinitely without charge, subject to occasional judicial review, the Obama administration has said.